X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 281.0
Details 1.5M ammonium sulfate, 0.0025M thiamine diphosphate, 0.0025 mM magnesium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 132.11 α = 90
b = 145.44 β = 90
c = 147.98 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 225 mm -- 2006-12-06
Diffraction Radiation
Monochromator Protocol
Double crystal Si[111], horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.93001 EMBL/DESY, Hamburg X12

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.12 99 99.8 0.107 -- -- 7.0 -- 80614 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.12 2.16 99.9 0.739 -- -- 5.6 4002

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.12 18.31 -- 0.0 -- 78322 3939 97.16 -- 0.195 0.193 0.237 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.12 2.174 5765 299 5466 0.258 0.302 -- 98.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.972
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.023
r_scangle_it 4.438
r_xyhbond_nbd_refined 0.146
r_scbond_it 2.982
r_gen_planes_refined 0.009
r_symmetry_vdw_refined 0.236
r_mcangle_it 1.779
r_metal_ion_refined 0.038
r_nbtor_refined 0.309
r_dihedral_angle_2_deg 38.586
r_dihedral_angle_3_deg 15.374
r_dihedral_angle_1_deg 6.36
r_mcbond_it 1.139
r_angle_refined_deg 1.908
r_symmetry_hbond_refined 0.188
r_dihedral_angle_4_deg 19.121
r_chiral_restr 0.128
r_nbd_refined 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8234
Nucleic Acid Atoms 0
Heterogen Atoms 131
Solvent Atoms 433

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345dtb data collection
HKL-2000 data reduction
HKL-2000 data scaling